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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctctgatcatgttttgttcatcacagttatttttctgtttatcacacagactatctcattcatgttatttttatttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG

Basic information

species Glycine max
transcript GLYMA20G24070.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 13
-----gtctctgatcatgttttgttcatcacagttatttttctgtttat-cacacagactatctcattcatgttatttttatttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG
        |  ||     |    || ||  || |||   |   |   || |  ||||   | |||||| ||| | |||     | || ||||| ||||| || ||||| ||||| |||||||||||||| |||||||| || || ||||| || || || || |||||||| |||
gtaaacatttggactccatacatttgatttcatttaagctatggcaaatacttacagtggagctcatttatgctgtttca---tgttacagCTTTATGCCAACTATGCAATTGGGAAGGATGTCCAGGCCATGAAAGCCGTTGTGGGAGAGGAGGCGCTCTCTTCTGAGGATCTG

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 12
gtctctgatcatgttttgttcatcacagttatttttctgtttatcacacagactatctcattcatgttatttttatttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG
     |    ||  |  || |||     || ||||      |       |   |     ||| |  |    | | || | ||||||| ||||| || |||||||||||||||||||| ||||| ||||| || || |||||||| || ||||| || |||||||| |||
----gtacctattatgagtccataggctttgttttcagacatgatgtgtaagatga---attgacatctactgttttctgttcagCTTTATGCCAACTATGCTATTGGAAAGGATGTTCAGGCCATGAAGGCTGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 13
----------------------gtctctgatcatgttttgttca-tcacagttatttttctgtttatcacacagactatctcattcatgt-tatttttatttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG
                       | | |||| | |   |    | ||   | ||   ||| |   || |     |  ||   ||| |  | |  | || | | |||||||| ||||| || || || |||||||||||||| ||||| ||||| ||||| |||||||| || ||||| || |||||||| |||
gtacatactatgagtccatgttatttttgataagggagtccatagtctttgctacccttcagac-atgatgtgcaagatga-attgacatctgctgttttctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 14
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 14
------------------------------gtctctgatcatgttttgttcatcacagtt--atttttctgtttatcacac---agactatctcattcatgttatttttatttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG
                               |  | ||  | | |||||| ||   ||||  | || ||   || |    |   ||  || ||  || ||  | ||||| |  ||| ||| | ||||| ||||| |||||||||||||| || ||||| |||||||| ||||||||||||||||| ||||| || ||||| |||
gtaagactttatttcttgtccattaccagcattgcagaa-aagctttgtttatgtaagttttacttgtcaacttttttagcctgagcttaacttgtt-attatgtttttgtgattt-cagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTG

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 13
gtctctgatcatgttttgttcatcacagttatttttctgtttatcacacagactatctcattcatgttatttttatttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG
        |  | |||  |   |    | |   ||    ||          ||   |  | | |||  ||| ||  || ||||||||||||||||||||||| ||||| |||||||| || ||||||||||| ||||||||||||||||||||||| |||||||| |||
-------gtagtatttgat--gttcgggctgcgttcaccttctctttgagcacgtcccaactaatgcgattctt-cttctttcagCTCTATGCAAATTATGCAATTGGGAAGGATGTTCAAGCAATGAAAGCTGTGGTTGGAGAAGAAGCACTTTCTTCTGAGGATCTG

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 14
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 13
-----------gtctctgatcatgttttgttcatcacagttatttt----tctgtttatcacacagactatctcattcatgttatttttatttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG
             |    | | | |   || | | |    ||||      || |      | |  ||   |     | |  | || |||   | |  ||| | ||||| |||||||| |||||||||||||| || |||||||| || || |||||||| |||||  | || || || || |||
tttttgtttcaagcatgcaacttctcaagtgcctaatgcctattacgaaatcaggaatggatagggaacttacacctaacatcatgtttgcctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTG

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 14
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 12
--------------gtctctgatcat-gttttgttcatcacagttatttt-tctgtttatcacacagactatctcattcatgttatttttatttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG
               | | ||  |||    ||   |||     | ||    |||| ||    || ||||| |    || |  |  | | ||    || ||| | || ||||| ||||| |||||||||||||| || || ||||| || ||||| |||||||||||  | || || ||||| |||
cacatgagagcatcatttgtggccatcaacttccccatttttctgatgaagtctgcttgagtca-agactttgggtttaacatggtgtctacccattgcagTTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTG

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 14
lower sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 12
gtctctgatcatgttttgttcatcacagttatttttctgtttatcacacagactatctcattcatgttatttttatttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG
                                || | | |  ||||   |  |  |    || |   | | |     |||| |||||||||||||| ||||| ||||| || || || || || |||||||| || || ||||||||||| || |||||||| || |||
------------------------gtgagcgattgtgtctacatcat-tatgccgt----ttaacactgtctactggttttgcagCTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 14
lower sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 12
gtctctgatcatgttttgttcatcacagttatttttctgtttatcacacagactatctcattcatgttatttttatt--tttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG
                                || | | |  ||||       |||  | || |    || | || |  |||| ||||| |||||||| ||||| ||||| || || || || || |||||||| || || ||||||||||| || |||||||| || |||
------------------------gtgagcgattgtgtctacatca------ttatgccgttta-acaatgtctactggttttgcagCTTTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|120495604|gb|EH223771.1|EH223771
EST:     CTATTGGTGAGGGAATGACTAGAAGGGATCATTCTGATGTGTCCAACCAG                         CTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTG
genomic: CTATTGGTGAGGGAATGACTAGAAGGGATCATTCTGATGTGTCCAACCAGgtctctgatc ... tttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTG
EST: gi|21256304|gb|BQ453192.1|BQ453192
EST:     CTATTGGTGAGGGAATGACTAGAAGGGATCATTCTGATGTGTCCAACCAG                         CTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTG
genomic: CTATTGGTGAGGGAATGACTAGAAGGGATCATTCTGATGTGTCCAACCAGgtctctgatc ... tttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTG
EST: gi|16279439|gb|BI943437.1|BI943437
EST:     CTATTGGTGAGGGAATGACTAGTATGGATCATTCTGATGTGTCCAACCAG                         CTCTATGCAAATTATGCTATTGGA
genomic: CTATTGGTGAGGGAATGACTAGAAGGGATCATTCTGATGTGTCCAACCAGgtctctgatc ... tttttttcagCTCTATGCAAATTATGCTATTGGA
EST: gi|16276744|gb|BI942021.1|BI942021
EST:     CTATTGGTGAGGGAATGACTAGAAGGGATCATTCTGATGTGTCCAACCAG                         CTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTG
genomic: CTATTGGTGAGGGAATGACTAGAAGGGATCATTCTGATGTGTCCAACCAGgtctctgatc ... tttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTG
EST: gi|37996030|gb|CF807619.1|CF807619
EST:     CTATTGGTGAGGGAATGACTAGAAGGGATCATTCTGATGTGTCCAACCAG                         CTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTG
genomic: CTATTGGTGAGGGAATGACTAGAAGGGATCATTCTGATGTGTCCAACCAGgtctctgatc ... tttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTG
EST: gi|15001046|gb|BI321860.1|BI321860
EST:     CTATTGGTGAGGGAATGACTAGAAGGGATCATTCTGATGTGTCCAACCAG                         CTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTG
genomic: CTATTGGTGAGGGAATGACTAGAAGGGATCATTCTGATGTGTCCAACCAGgtctctgatc ... tttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTG
EST: gi|16278548|gb|BI942962.1|BI942962
EST:     TATTGGTGAAGGAATGACTAGAAGGGATCATTCTGATGTGTCCAAACC-G                         CTATATGCCAATTATGCTATTTGAAACGATGTCCCGGCAATGAAAGCAGT
genomic: TATTGGTGAGGGAATGACTAGAAGGGATCATTCTGATGTGTCCAA-CCAGgtctctgatc ... tttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGT
EST: gi|21601974|gb|BQ612305.1|BQ612305
EST:     CTATTGGTGAGGGAATGACTAGAAGGGATCATTCTGATGTGTCCAACCAG                         CTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTG
genomic: CTATTGGTGAGGGAATGACTAGAAGGGATCATTCTGATGTGTCCAACCAGgtctctgatc ... tttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTG
EST: gi|19269615|gb|BM885871.1|BM885871
EST:     CTATTGGTGAGGGAATGACTAGAAGGGATCATTCTGATGTGTCCAACCAG                         CTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTG
genomic: CTATTGGTGAGGGAATGACTAGAAGGGATCATTCTGATGTGTCCAACCAGgtctctgatc ... tttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttctgtttatcacacagactatctcattcatgttatttttatttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG
                                    ttatttttattttttt  CT-rich tract
                       tatctcattcatgtta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctctgatcatgttttgttcatcacagttatttttctgtttatcacacagactatctcattcatgttatttttatttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC